Re: [AMBER] # of Coordinates Mismatch in PCA

From: Kenneth Huang <khuang8.student.gsu.edu>
Date: Mon, 13 Aug 2018 03:21:38 +0000

Hi,


I think the problem might becoming up from the datasets that it's calling on-


crdaction full_no_waters.mdcrd projection full_no_waters_projection3 modes myEvecs beg 1 end 3 :38-318&!.H=


Looks like it's trying to call on the original trajectory that isn't modified to fit what the evecs file is based off of (:38-318&!.H=)- you can check by seeing if the prmtop total number of atoms is the same as 10983.


Try this instead- it should be the same thing, but without the crdaction parts:


trajin full_no_waters.mdcrd
reference Crystal_Structure_with_Hydrogens.pdb
rms ref Crystal_Structure_with_Hydrogens.pdb :38-318&!.H
matrix covar name full_no_waters_covar :38-318&!.H
runanalysis diagmatrix full_no_waters_covar out full_no_waters_evecs.dat vecs 3 name myEvecs nmwiz nmwizvecs 3 nmwizfile protein.nmd nmwizmask :38-318&!.H
projection evecs myEvecsut PCA.project.dat beg 1 end 3 :38-318&!.H
run
quit

Best,

Kenneth

________________________________
From: Robert Molt <rwmolt07.gmail.com>
Sent: Sunday, August 12, 2018 1:04 AM
To: AMBER Mailing List
Subject: [AMBER] # of Coordinates Mismatch in PCA

Good morning,

I am attempting to perform a principle component analysis but am
encountering an unexpected error during the projection step using cpptraj:

Error: number selected coords (5865) != number avg coords (10983) in myEvecs

In short, I am confused how a mismatch could occur. My understanding is
that if my eigenvectors (myEvecs) come directly from the covariance
matrix of a given trajectory, no mismatch should be possible (if I have
consistent masks). I must be confused and seek clarification.

I am using cpptraj v. 15. I am following the tutorial specified on

https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.amber.utah.edu%2FAMBER-workshop%2FLondon-2015%2Fpca%2F&amp;data=02%7C01%7Ckhuang8%40student.gsu.edu%7C7fc1a367c0fd472af3e308d6001134ce%7C704d822c358a47849a1649e20b75f941%7C0%7C0%7C636696471236703076&amp;sdata=h%2BdSn8RuhBydNGsW1J1NDsQIbMZabo46A3mJmDV5aBQ%3D&amp;reserved=0

My cpptraj commands are (in blue), with trivial warning messages listed
(in red):

trajin full_no_waters.mdcrd
reference Crystal_Structure_with_Hydrogens.pdb

Warning: PDB line length is short (67 chars, expected 80).
Warning: PDB Crystal_Structure_with_Hydrogens.pdb: Reading frame 2, got
711 atoms, expected 4431.
Warning: Only using frames 1-1

createcrd full_no_waters.mdcrd
run
crdaction full_no_waters.mdcrd rms ref
Crystal_Structure_with_Hydrogens.pdb :38-318&!.H

Warning: Coordinates are being rotated and box coordinates are present.
Warning: Unit cell vectors are NOT rotated; imaging will not be possible
Warning: after the RMS-fit is performed.

crdaction full_no_waters.mdcrd matrix covar name full_no_waters_covar
:38-318&!.H
runanalysis diagmatrix full_no_waters_covar out full_no_waters_evecs.dat
vecs 3 name myEvecs nmwiz nmwizvecs 3 nmwizfile protein.nmd nmwizmask
:38-318&!.H

Up to this point, the warnings listed are trivial and everything seems
fine. I then give the command

crdaction full_no_waters.mdcrd projection full_no_waters_projection3
modes myEvecs beg 1 end 3 :38-318&!.H=

Error: number selected coords (5865) != number avg coords (10983) in myEvecs 


--
Dr. Robert Molt Jr.
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Received on Sun Aug 12 2018 - 20:30:02 PDT
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